Comparative analysis of annotation pipelines using the first Japanese white-eye (Zosterops japonicus) genome

Introduced into Hawaii in the early 1900s, the Japanese white-eye or warbling white-eye (Zosterops japonicus) is now the most abundant land bird in the archipelago. Here, we present the first Z. japonicus genome, sequenced from an individual in its invasive range. This genome provides an important resource for future studies in invasion genomes. We annotated the genome using two workflows: standalone AUGUSTUS and BRAKER2. We found that AUGUSTUS was more conservative with gene predictions when compared to BRAKER2. The final number of annotated gene models was similar between the two workflows, but the standalone AUGUSTUS had over 70 percent of gene predictions with Blast2GO annotations versus 20 percent using BRAKER2. Additionally, we tested whether using RNAseq data from 47 samples had a significant impact on annotation quality when compared to data from a single sample, as generating RNAseq data for genome annotation can be expensive and requires well preserved tissue. We found that more data did not significantly change the number of annotated genes using AUGUSTUS but using BRAKER2 the number increased substantially. The results presented here will aid researchers in annotating draft genomes of non-model species as well as those studying invasion success.